All libraries (n = 18) were pooled in equimolar amounts and loaded at 250 pM onto a single Illumina NovaSeq S4 flow cell lane for 2x150 bp sequencing at Genewiz (South Plainfield, NJ). This was estimated to yield 111-138 M reads per library and 99-123x coverage of the P. acuta genome (3.3 M bp) and 38-47x coverage of the M. capitata genome (8.8 M bp), assuming 100% even coverage (e.g., 150 bp read * 2 pairs * 111 M reads/336,684,533 bp for P. acuta).
Sequence quality was checked by FastQC v0.11.8 and adapters from paired-end sequences were trimmed using TrimGalore! version 0.4.5 (Krueger 2012) . Following recommendations for methylation sequence analysis from the manufacturer's protocol and from the Bismark User Guide, 10 bp were hard trimmed from the 5' and 3' end of each read for WGBS and MBDBS samples, and RRBS samples were trimmed with --non_directional and --rrbs options. Bisulfite-converted genomes were created insilico with Bowtie 2-2.
Sequence quality was checked by FastQC v0.11.8 and adapters from paired-end sequences were trimmed using TrimGalore! version 0.4.5 (Krueger 2012) . Following recommendations for methylation sequence analysis from the manufacturer's protocol and from the Bismark User Guide, 10 bp were hard trimmed from the 5' and 3' end of each read for WGBS and MBDBS samples, and RRBS samples were trimmed with --non_directional and --rrbs options. Bisulfite-converted genomes were created insilico with Bowtie 2-2.